When Alice is crawling out of the White Rabbit's house after being shrunk, the door is shut. When she runs to the step, the door is open.
During "The Walrus and the Carpenter", the appearance of the walrus' eyes is inconsistent between shots. Some shots have just little black dot eyes, while some shots have him with full pupils and colored eyes.
In the oyster story, the oyster family's calendar changes between shots.
At the beginning of "The Walrus and the Carpenter", the walrus' cigar disappears and reappears in between shots of him on his way to visit the oysters.
Just before the flowers sing "All in the Golden Afternoon", we see an orange dandelion tuning up. Between him are two other dandelions, one purple one on the left, and one red one on the right. Two shots later, when the scat-singing begins, the two dandelions have switched places.
In the opening credits, the name of the first "Alice" book is given as "The Adventures of Alice in Wonderland" rather than "Alice's Adventures in Wonderland".
The Caterpillar's colors are reversed when he says "Keep your temper." Normally, his body is blue-violet and his belly is light blue, but for that shot the body is light blue and the belly is blue-violet. Many creatures of reality as well as fantasy have color changing abilities.
During the tea party, the "half a cup" changes its configuration, and the seating arrangement changes when the March Hare is smacked with a hammer. Although probably not intentional, these goofs fit in with the absurd, disorienting humor of the scene.
The size-changing mushroom appears to be Entoloma undatum, a deadly toxic species, but is in fact a fantasy species found only in Wonderland.
When the Caterpillar changes, he loses his arms and legs. During the chase scene at the end of the movie, when Alice swims up to him on his floating mushroom, his arms and legs are back. This is part of his biology.
At the start of the film, Alice is sitting on a tree branch as her sister Lorina sits at the base of the tree reading aloud, but when Alice wakes up at the end of the film, she is sitting in Lorina's spot and Lorina is standing up. It is possible that Alice fidgeted and moved around significantly while in "Wonderland", and Lorina changed her own position accordingly.
At the tea party, when the March Hare smashes the White Rabbit's pocket watch with a hammer, the image briefly changes to black and white.
Towards the end of the scene with the flowers, the flowers are asking Alice what kind of flower she is. There's a shot from above, looking down on Alice. Behind her, we see her shadow on the ground. Although Alice is moving a bit, the shadow is perfectly still.
Many of the voice actors who played minor roles are uncredited as the end credits are only mentioning those who voiced major roles.
Tweedle Dum and Tweedle Dee make the honking sounds of "honk" and "beep" respectively similar to car horns. However, considering the setting to be set presumably in the 1860s like the fairytale it was adapted from was originally published, car horns did not exist until 1908.
When Alice eats the cookie in the White Rabbit's house and grows, she says, "Oh, no, no, not again!" Alice's mouth does not move to these words.
While Alice becomes a giant inside the White Rabbit's house in the process, only her right leg goes through the door leading from the White Rabbit's bedroom and down the stairs and out the front door without an explanation about how her left leg was able to go through and out another door.
At the beginning of "All in the Golden Afternoon" when Rose says, "Sound your A, Lily", Lily sings B-flat, not A.
In the song "Painting the Roses Red", after Alice sings "Oh, pardon me, but Mister Three, why must you paint them red?" the three cards say "Huh? Ohhhhhhh!". When they say that, The three of clubs card has a three in the bottom right corner with no clubs symbol on top of the three. the three of clubs also has nothing in the top left corner. The ace and two of clubs have nothing in both of their corners. A few slides later, the symbols in the corners come back. (Possibly a chameleon-ability similar to the Caterpillar.)